1.96.0

Added

• Morphology and electrophysiology facets for global study search (#2251)
• More human pathways for search and visualization (#2260, #2264)
• "Parse Evercode WT v3" and "Mini" version to menu in upload UI (#2262)

Changed

• Omit CELLxGENE IDs from cell facets (#2258)
• Update to sentry-ruby gem for error reporting (#2256)
• Bump rack from 2.2.13 to 2.2.14 (#2254)

Fixed

• Null filter edge case (#2258)
• Search via DE genes click (#2259)
• Gene popover for mouse in related genes ideogram (#2260)

1.95.1

Fixed

• Gene-list paste search in study views not eligible for pathways (#2252)

1.95.0

Added

• Search and visualize biological pathways (#2206, #2248, #2249)
• Adding reporting email for studies over 200 GB (#2247)

Changed

• Bump net-imap from 0.5.6 to 0.5.7 (#2246)

Fixed

1.94.0

Added

• Extend CSFV ontology validation to all metadata files (#2242)

Changed

• Update all GHA runners to ubuntu-24.04 (#2239)
• Bump vite from 4.5.10 to 4.5.13 (#2240)
• Bump nokogiri from 1.18.4 to 1.18.8 (#2244)

Fixed

• Fix failure metrics for AnnData ingest (#2243)

1.93.1

Fixed

• Restore SCP-computed DE for classic uploads, via scp-ingest-pipeline:1.41.3 (SCP-5984)
• Ensure ingest works when EBI OLS is down (#2236)

1.93.0

Added

• Support for specifying location of raw count data in visualization AnnData files (#2232)
• PIP-seq as option for library preparation protocol (#2234)

Changed

• Removed unused/deprecation Terra orchestration API endpoint integrations (#2233)

Fixed

• Make updating existing DE result more robust (#2228)
• Updated broken NeMO tests (#2229)
• Stop forcing isAuthorDe on pairwise results (#2230)

1.92.1

Changed

• Updating to rails-baseimage:3.0.0 (#2221, #2224)
  • Ubuntu 24.04
  • Ruby 3.4
  • Nginx 1.24
  • Passenger 6.0.2

Fixed

• Correctly identify bundled files in upload wizard (#2222)
• Update reference study metadata file (#2225)

1.92.0

Added

• Support upload, visualization of CSI as BED index file format (#2203)
• API integration for user-submitted differential expression calculations (#2212)
• Scripts for automating scheduled instance restarts (#2216)

Changed

• Simplifying parse_status flag logic (#2210)
• Updates to NeMO-specific ImportService functionality (#2214)

Fixed

• Address issues in automated DE submission for AnnData files (#2213)

1.91.0

Added

• Support upload, visualization of CSI as BED index file format (SCP-5920)
• Improve error UX in study creation (SCP-5933)

Changed

• Remove nightly storage integrity check (#2205)
• Allow sequence file upload for AnnData UX (#2203)
• Updating to scp-ingest-pipeline:1.40.1 (#2207)

1.90.0

Added

• Updated terms of service re: data retention, embargoes (#2195)
• Enhance DE selection UI (feature flagged, #2197)

Changed

• Set max length of study embargoes to 2 years from study creation (#2195)
• Bump net-imap to 0.5.6 (#2199)